Assess RNA Structure (Example)

File: 1a9n.pdb
Size: 0.04 MB
No. of Residues: 24 nts
File: PDB filename.

Size: PDB file size (in megabytes).

No. of Residues: Total number of nucleotides in the structure.

Chain: Chain selected by the user to calculate the energy profile (if multiple chains are present in the file, the user must select one).

Potential: Knowledge-based potential used to calculate the total score and the energy profile. For a detailed description of the different potentials available, please read our previous publication where the potentials were assessed and validated (follow this link).

-CG (C3p): Coarse-grain potential that takes into account interactions between C3p carbons only (i.e. four atom types, one for each nucleotide).

-BB only: Backbone potential that calculates the energy scores considering the interactions between atoms O3p, C3p, C4p, C5p, O5p, P, OP1, OP2 and OP3 (i.e. 36 atom types, 9 for each nucleotide).

-BB+Rb: Backbone and ribose potential that calculates the energy score based on the interaction between atoms of the backbone (see BB only potential described above) and the rest of the ribose atoms: C1p, C2p and O4p (48 atom types, 12 for each nucleotide).

-Full atom: Potential that contains a definition of energy score for pairwise interactions of all non-hydrogen atoms in the four canonical nucleotides.

Include modified residues? (available only in case the structure has modified residues): option for including non-canonical nucleotides in the total energy score and energy profile calculation. The atom type definition in this case is adopted based on the closest standard nucleotide. It is important to note that energy calculations for non-standard or modified residues is only approximate and may miss some undefined atom types.

Window: number of nucleotides used to average the energy score values in the profile.